                      :-) GROMACS - gmx mdrun, 2021.5 (-:

                            GROMACS is written by:
     Andrey Alekseenko              Emile Apol              Rossen Apostolov     
         Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
       Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
     Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
    Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
       Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
      Aleksei Iupinov           Christoph Junghans             Joe Jordan        
    Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
      Carsten Kutzner              Per Larsson              Justin A. Lemkul     
       Viveca Lindahl            Magnus Lundborg             Erik Marklund       
        Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
        Szilard Pall               Sander Pronk              Roland Schulz       
       Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
       Peter Tieleman              Jon Vincent              Teemu Virolainen     
     Christian Wennberg            Maarten Wolf              Artem Zhmurov       
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2021.5
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /media/romi/LACIE/July 31/5hdq (2)/5hdq-313k
Process ID:   176218
Command line:
  gmx mdrun -deffnm md_1_20 -cpi md_0_10.cpt -noappend -v

GROMACS version:    2021.5
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        disabled
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 9.4.0
C compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 9.4.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops SHELL:-fopenmp -O3 -DNDEBUG


Running on 1 node with total 20 cores, 20 logical cores
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  12th Gen Intel(R) Core(TM) i7-12700K
    Family: 6   Model: 151   Stepping: 2
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Only logical processor count


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.5850051
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 50050000
   init-step                      = 0
   simulation-part                = 1
   mts                            = false
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = 1352544977
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 96
   fourier-ny                     = 96
   fourier-nz                     = 96
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
grpopts:
   nrdf:     28250.8      440190
   ref-t:         313         313
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0


Reading checkpoint file md_0_10.cpt
  file generated by:     /usr/bin/gmx
  file generated at:     Sat Jun 17 04:24:32 2023

  GROMACS double prec.:  0
  simulation part #:     1
  step:                  50000000
  time:                  100000.000000

  Version mismatch,
    current program: 2021.5
    checkpoint file: 2019.6

The current GROMACS major version is not identical to the one that
generated the checkpoint file. In principle GROMACS does not support
continuation from checkpoints between different versions, so we advise
against this. If you still want to try your luck we recommend that you use
the -noappend flag to keep your output files from the two versions separate.
This might also work around errors where the output fields in the energy
file have changed between the different versions.

Changing nstlist from 10 to 50, rlist from 1 to 1.114


Initializing Domain Decomposition on 20 ranks
Dynamic load balancing: auto
Using update groups, nr 79072, average size 2.9 atoms, max. radius 0.139 nm
Minimum cell size due to atom displacement: 0.418 nm
Initial maximum distances in bonded interactions:
    two-body bonded interactions: 0.446 nm, LJ-14, atoms 6845 7648
  multi-body bonded interactions: 0.494 nm, CMAP Dih., atoms 5719 5735
Minimum cell size due to bonded interactions: 0.544 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Guess for relative PME load: 0.20
Will use 16 particle-particle and 4 PME only ranks
This is a guess, check the performance at the end of the log file
Using 4 separate PME ranks, as guessed by mdrun
Optimizing the DD grid for 16 cells with a minimum initial size of 0.680 nm
The maximum allowed number of cells is: X 17 Y 17 Z 15
Domain decomposition grid 4 x 4 x 1, separate PME ranks 4
PME domain decomposition: 4 x 1 x 1
Interleaving PP and PME ranks
This rank does only particle-particle work.
Domain decomposition rank 0, coordinates 0 0 0

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 3.05 nm Y 3.05 nm

The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
(the following are initial values, they could change due to box deformation)
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   1.392 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 1.392 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.46 Y 0.46
The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   1.392 nm

Using 20 MPI threads
Using 1 OpenMP thread per tMPI thread

Pinning threads with an auto-selected logical core stride of 1
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073

Generated table with 1056 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: <C6> 3.1280e-04


Using SIMD 4x8 nonbonded short-range kernels

Using a dual 4x8 pair-list setup updated with dynamic pruning:
  outer list: updated every 50 steps, buffer 0.114 nm, rlist 1.114 nm
  inner list: updated every 12 steps, buffer 0.002 nm, rlist 1.002 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 50 steps, buffer 0.244 nm, rlist 1.244 nm
  inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 5568

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


Linking all bonded interactions to atoms


Intra-simulation communication will occur every 10 steps.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 231368 Atoms
Atom distribution over 16 domains: av 14460 stddev 209 min 14232 max 14848
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

Started mdrun on rank 0 Thu Aug  1 10:52:26 2024

           Step           Time
       50000000   100000.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    9.53957e+03    2.58251e+04    1.66608e+04    1.48300e+03   -4.22057e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    8.28356e+03    1.68592e+05    5.00661e+05   -2.95859e+04   -3.77430e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.13065e+04   -3.05575e+06    6.08498e+05   -2.44726e+06    4.95408e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12464e+02   -2.07741e+02    6.63718e+01    4.27236e-06


DD  step 50000049 load imb.: force 36.3%  pme mesh/force 1.900
step 50000300: timed with pme grid 96 96 96, coulomb cutoff 1.000: 10721.2 M-cycles
step 50000400: timed with pme grid 80 80 80, coulomb cutoff 1.169: 14284.3 M-cycles
step 50000500: timed with pme grid 84 84 84, coulomb cutoff 1.113: 11628.1 M-cycles
step 50000600: timed with pme grid 96 96 96, coulomb cutoff 1.000: 11431.9 M-cycles
              optimal pme grid 96 96 96, coulomb cutoff 1.000


Received the INT signal, stopping within 50 steps

           Step           Time
       50001550   100003.10000

Writing checkpoint, step 50001550 at Thu Aug  1 10:54:42 2024



-------------------------------------------------------
Program:     gmx mdrun, version 2021.5
Source file: src/gromacs/mdlib/mdoutf.cpp (line 413)
MPI rank:    0 (out of 20)

File input/output error:
Cannot fsync 'md_1_20.part0002.log'; maybe you are out of disk space?

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
